Spatially-Resolved Top-down Proteomics Bridged to MALDI MS Imaging Reveals the Molecular Physiome of Brain Regions

Delcourt, Vivian; Franck, Julien; Quanico, Jusal; Gimeno, Jean-Pascal; Wisztorski, Maxence; Raffo-Romero, Antonella; Kobeissy, Firas; Roucou, Xavier; Salzet, Michel; Fournier, Isabelle

doi:10.1074/mcp.m116.065755

Cited by 40 publications

(46 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In human cells, AltProt identification was occasionally reported then ( 69 ), but this mechanism has long been considered as anecdotal in eukaryotes. Nonetheless, based on the tremendous increase of large-scale proteomic and transcriptomic studies over the last decade, we ( 2 , 12 , 13 ) and other teams ( 6 , 70 ) were able to demonstrate the presence of AltORF-encoded proteins. The discovery of this ‘ghost’ proteome inherently raised many questions about the potential function exerted by these small proteins and how to analyse and predict their role through large-scale and unsupervised analysis.…”

Section: Discussionmentioning

confidence: 92%

“…The implementation of AltProt database interrogation in large-scale proteomic experiments has opened the way to their massive identification moving forward with the characterization of their physiological and physiopathological role [e.g. ovarian cancer ( 12 ), brain physiome ( 13 ) and viral infection ( 14 )]. Not only AltProts are believed to have a central role in signalling pathways, but it was also demonstrated that some of them (e.g.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Alternative proteins are functional regulators in cell reprogramming by PKA activation

Cardon

Franck

Coyaud

et al. 2020

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

It has been recently shown that many proteins are lacking from reference databases used in mass spectrometry analysis, due to their translation templated on alternative open reading frames. This questions our current understanding of gene annotation and drastically expands the theoretical proteome complexity. The functions of these alternative proteins (AltProts) still remain largely unknown. We have developed a large-scale and unsupervised approach based on cross-linking mass spectrometry (XL-MS) followed by shotgun proteomics to gather information on the functional role of AltProts by mapping them back into known signalling pathways through the identification of their reference protein (RefProt) interactors. We have identified and profiled AltProts in a cancer cell reprogramming system: NCH82 human glioma cells after 0, 16, 24 and 48 h Forskolin stimulation. Forskolin is a protein kinase A activator inducing cell differentiation and epithelial–mesenchymal transition. Our data show that AltMAP2, AltTRNAU1AP and AltEPHA5 interactions with tropomyosin 4 are downregulated under Forskolin treatment. In a wider perspective, Gene Ontology and pathway enrichment analysis (STRING) revealed that RefProts associated with AltProts are enriched in cellular mobility and transfer RNA regulation. This study strongly suggests novel roles of AltProts in multiple essential cellular functions and supports the importance of considering them in future biological studies.

show abstract

Section: Discussionmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Alternative proteins are functional regulators in cell reprogramming by PKA activation

Cardon

Franck

Coyaud

et al. 2020

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

show abstract

“…Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) is a powerful analytical technique widely used for analysis of proteins in a broad range of biological samples which vary from lysed cells extracts [1][2][3][4][5][6][7][8][9][10] to tissue sections [11][12][13][14][15][16][17][18]. Whole cell MALDI fingerprinting is based on the mass spectral analysis of a whole cell without additional preparatory steps such as fractionation or extraction.…”

Section: Introductionmentioning

confidence: 99%

Whole Cell MALDI Fingerprinting Is a Robust Tool for Differential Profiling of Two-Component Mammalian Cell Mixtures

Petukhova

Young

Wang³

et al. 2018

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

MALDI fingerprinting was first described two decades ago as a technique to identify microbial cell lines. Microbial fingerprinting has since evolved into an automated platform for microorganism identification and classification which is now routinely used in clinical and environmental sectors. The extension of fingerprinting to mammalian cells has yet to progress partly due to compartmentalization of eukaryotic cells and overall higher cellular complexity. A number of publications on mammalian whole cell fingerprinting suggests that the method could be useful for classification of different cell types, cell states, and monitoring cell differentiation. We report the optimization of MALDI fingerprinting workflow parameters for mammalian cells and its application for differential profiling of mammalian cell lines and two component cell line mixtures. Murine fallopian tube cells and high-grade ovarian carcinoma cell lines and their mixtures are used as model mammalian cell lines. Two-component cell mixtures serve to determine the method's feasibility for complex biological samples as the ability to detect cancer cells in a mixed cell population. The level of detection of cancer cells in the two-component mixture by principle component analysis (PCA) starts to deteriorate at 5% but with application of a different statistical approach, Wilcoxon rank sum test, the level of detection was determined to be 1%. The ability to differentiate heterogeneous cell mixtures will help further extend whole cell MALDI fingerprinting to complex biological systems.

show abstract

“…Finally, identified AltProts are found to be translated, either from mRNA including from the non-coding 5′ & 3′ UTR or a frame shift (+1 or 2 nucleotides) in the CDS of the RefProt, or from non-coding RNA (ncRNA) [9]. Overall, largescale bottom-up [9][10][11][12] and top-down [13,14] proteomics have enable the identification of an important number of these AltProts. Very importantly, AltProts were also shown to be functional and carrying important cell functions [12,[15][16][17].…”

Section: Introductionmentioning

confidence: 99%

SARS-Cov-2 Interactome with Human Ghost Proteome: A Neglected World Encompassing a Wealth of Biological Data

Cardon¹,

Fournier²,

Salzet³

2020

Preprint

Self Cite

View full text Add to dashboard Cite

Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics has led to a massive identification of proteins translated from mRNAs of alternative ORF (AltORFs), in addition to the predicted proteins issued from the reference ORF or from ncRNAs. These alternative proteins (AltProts) are not represented in the conventional protein databases and this “Ghost proteome” was not considered until recently. Some of these proteins are functional and there is growing evidence that they are involved in central functions in physiological and physiopathological context. Based on our experience with AltProts we have got interested in finding out their involvement in development of the SARS-CoV-2 virus, responsible for the 2020 Covid-19 outbreak. Thus, we have scrutinized the recently published data by Krogan and coworkers (2020) on the SARS-CoV-2 interactome with host cells by co-IP in the perspective of drug repurposing. The initial work has revealed the interaction between 332 human cellular RefProts with the 27 viral proteins. Re-interrogation of this data using 23 viral targets and including AltProts, followed by enrichment of the interaction networks, leads to identify 218 RefProts (in common to initial study) plus 56 AltProts involved in 93 interactions. This demonstrates the necessity to take into account the Ghost proteome for discovering new therapeutic targets and establish new therapeutic strategies. Missing the ghost proteome in the drug metabolism and pharmacokinetic (DMPK) drug development pipeline will certainly be a major limitation to the establishment of efficient therapies.

show abstract

Spatially-Resolved Top-down Proteomics Bridged to MALDI MS Imaging Reveals the Molecular Physiome of Brain Regions

Cited by 40 publications

References 67 publications

Alternative proteins are functional regulators in cell reprogramming by PKA activation

Alternative proteins are functional regulators in cell reprogramming by PKA activation

Whole Cell MALDI Fingerprinting Is a Robust Tool for Differential Profiling of Two-Component Mammalian Cell Mixtures

SARS-Cov-2 Interactome with Human Ghost Proteome: A Neglected World Encompassing a Wealth of Biological Data

Contact Info

Product

Resources

About